This protein is responsible for the synthesis of pseudouridine from uracil-55 in the ψGC loop of transfer RNAs.
KEGG: ppr:PBPRA0614
STRING: 298386.PBPRA0614
Photobacterium profundum is a deep-sea Gammaproteobacterium belonging to the family Vibrionaceae. It is particularly notable as a model organism for studying adaptations to extreme environments. P. profundum strain SS9, originally isolated from the Sulu Sea in 1986, is characterized by optimal growth at 15°C and 28 MPa (approximately 280 atmospheres), making it both a psychrophile and piezophile (pressure-loving organism) .
The bacterium has rod-shaped cells measuring 2-4μm in length and 0.8-1.0μm in width, with a single unsheathed flagellum. Its genome consists of two circular chromosomes, similar to other members of the Photobacterium genus . The ability of P. profundum to thrive under high hydrostatic pressure makes its molecular machinery, including truB, particularly interesting for understanding adaptations to extreme conditions.
Beyond strain SS9, there are three other cultured wild-type strains: 3TCK (isolated from San Diego Bay, with optimal growth at 9°C and 0.1 MPa), DSJ4 (from the Ryukyu Trench at 5110m depth, with optimal growth at 10°C and 10 MPa), and strain 1230 . This diversity of growth optima allows for comparative studies of pressure adaptation mechanisms.
TruB is an enzyme that catalyzes the site-specific isomerization of uridine to pseudouridine at position 55 in the TΨC loop of tRNA molecules. This modification is one of the most evolutionarily conserved RNA modifications found across all domains of life .
The TruB enzyme from P. profundum specifically functions by:
Recognizing the TΨC stem-loop structure in tRNA
Catalyzing the rotation of the uracil base at position 55
Breaking the N1-glycosidic bond
Reforming a C5-glycosidic bond to create pseudouridine
This isomerization does not alter the base-pairing properties of the nucleoside but enhances base stacking and stabilizes RNA secondary structure due to the additional hydrogen bonding capability of pseudouridine. While the deletion of truB in some organisms like E. coli does not prevent growth under standard conditions, it does reduce competitive fitness and impairs survival during temperature shifts, suggesting its importance for adaptation to environmental stresses .
Pseudouridine modification at position 55 in tRNA molecules significantly impacts both structural stability and functional properties through several mechanisms:
Enhanced Base Stacking: The C5-glycosidic bond in pseudouridine allows for improved base stacking interactions, which strengthens the tertiary structure of tRNA.
Additional Hydrogen Bonding: Pseudouridine contains an additional imino group (NH) that can form hydrogen bonds with water molecules, contributing to structural rigidity.
Stabilization of RNA Structure: Studies have shown that pseudouridine modifications increase the thermal stability of RNA helices and the melting temperature of tRNA, which may be particularly advantageous for organisms living under extreme conditions.
Conformational Rigidity: The presence of pseudouridine in the TΨC loop restricts conformational flexibility, potentially protecting tRNA from degradation under stress conditions.
Research with E. coli has demonstrated that while truB deletion mutants grow normally under standard conditions, they show competitive disadvantages during co-culture with wild-type strains and exhibit defects in surviving rapid temperature transitions (from 37°C to 50°C) . This suggests that the pseudouridine modification is particularly important during environmental stress, making it a potentially crucial adaptation for pressure-tolerant organisms like P. profundum.
Researchers can assess the enzymatic activity of recombinant P. profundum truB using several complementary approaches:
1. Radioactive Assay:
Synthesize [32P]UTP-labeled tRNA substrate via in vitro transcription
Incubate labeled substrate with purified truB enzyme
Extract and digest RNA with nuclease P1
Analyze resulting nucleotides via two-dimensional thin-layer chromatography (2D-TLC)
Compare against known pseudouridine standards
2. CMCT-Primer Extension Assay:
Treat RNA with N-cyclohexyl-N'-(2-morpholinoethyl)carbodiimide metho-p-toluenesulfonate (CMCT)
This reagent forms adducts with pseudouridine residues
Perform reverse transcription with a labeled primer
The CMCT-Ψ adduct causes reverse transcriptase to stop one nucleotide before the modified position
Analyze extension products on sequencing gels
Compare band patterns between truB-treated and control samples
3. HPLC Analysis:
Prepare tRNA substrate via in vitro transcription
Incubate with purified truB enzyme
Digest treated RNA to nucleosides
Analyze by high-performance liquid chromatography
Compare retention times with pseudouridine standards
4. Nearest Neighbor Analysis:
Synthesize RNA with one nucleotide radioactively labeled
Treat with truB enzyme
Digest with RNase T2 (which produces 3'-monophosphates)
Analyze products by 2D-TLC
Identify modified nucleotides by their position relative to the labeled nucleotide
For optimal activity assessment, researchers should consider:
Including appropriate positive and negative controls
Testing activity under different buffer conditions (pH 7.0-8.5)
Evaluating temperature dependence (10-37°C)
Assessing pressure effects on enzymatic activity (0.1-30 MPa)
To effectively study truB function under high pressure, researchers should implement specialized equipment and protocols:
High-Pressure Experimental Setup:
Hardware Requirements:
High-pressure vessels capable of maintaining stable pressures up to 70 MPa
Temperature control system (typically 0-25°C range for P. profundum studies)
Pressure generation system (hydraulic pump or gas booster)
Pressure monitoring devices with digital recording capabilities
Sample containment system (typically polyethylene transfer pipettes or polyethylene tubing sealed with no headspace)
Experimental Approaches:
In vitro enzymatic assays: Conduct standard truB activity assays in pressure-resistant containers
Growth studies: Compare growth of wild-type and truB mutant strains under various pressure conditions
Gene expression analysis: Extract RNA from cells grown under different pressures to assess truB expression levels
Protein stability studies: Analyze thermal and pressure denaturation profiles of purified truB
Protocol for High-Pressure Growth Experiments:
Prepare cultures in appropriate media (e.g., 2216 medium for marine bacteria)
Fill pressure-resistant containers completely to eliminate air bubbles
Seal containers without trapped air
Place in pressure vessel and pressurize to desired level (e.g., 0.1, 10, 28, 70 MPa)
Incubate at appropriate temperature (typically 15°C for SS9 strain)
Monitor growth by sacrificing parallel samples at designated timepoints
Gene Complementation Approach:
Based on studies with pressure-sensitive genes, it's important to note that different experimental setups may yield variable results. For instance, in P. profundum studies, when exconjugants were tested for high-pressure growth ability after gene complementation, they were typically incubated at 15°C for 3-5 days before results could be assessed .
P. profundum truB presents several distinctive features compared to its homologs from non-piezophilic organisms, reflecting adaptations to high-pressure environments:
Structural Comparisons:
Amino Acid Substitutions: Specific substitutions that favor protein stability under pressure, such as reduced void volumes and increased ion pairs
Modified Flexibility: Strategic distribution of rigid and flexible regions to accommodate pressure effects
Hydration Properties: Altered surface properties that modulate protein-water interactions under pressure
While the search results don't directly establish a relationship between truB activity and high-pressure growth in P. profundum specifically, evidence from related studies suggests important connections:
Key Observations:
In Alcanivorax dieselolei, a marine oil-degrading bacterium, truB expression was significantly upregulated (log2 fold change of 3.09) under mild hydrostatic pressure (10 MPa) compared to atmospheric pressure, making it one of the most enhanced genes in the entire transcriptome .
This upregulation suggests that tRNA modification by truB may be crucial for protein synthesis under pressure conditions.
Protein synthesis is known to be a pressure-sensitive process, with one of the most vulnerable steps being the binding of aminoacyl-tRNA to ribosomes, as it requires a conformational change leading to volume increase (an unfavorable process under pressure) .
The formation of pseudouridine at position 55 in tRNA likely plays a role in stabilizing tRNA structure under pressure conditions, potentially facilitating more efficient translation.
Hypothesized Mechanism:
Under high-pressure conditions, cellular processes involving volume increases are inhibited. Translation, particularly the binding of aminoacyl-tRNA to ribosomes, is sensitive to pressure because it involves conformational changes with positive volume changes. The pseudouridine modifications introduced by truB stabilize tRNA structure, potentially counteracting some pressure effects and maintaining translation efficiency.
In P. profundum specifically, truB activity may be part of a suite of adaptations that allow efficient protein synthesis under high pressure. While RecD function has been directly linked to high-pressure growth in P. profundum , the specific contribution of truB remains to be fully characterized through targeted gene deletion and complementation studies similar to those performed for RecD.
Based on established methods for generating gene deletions in P. profundum and related bacteria, the following approach is recommended for constructing and validating truB mutants:
Construction of truB Gene Disruption Mutants:
PCR Amplification of Target Sequence:
Cloning into Suicide Vector:
Conjugal Transfer:
Transform constructed plasmid into donor E. coli strain (e.g., MC1061 containing helper plasmids)
Perform conjugation with P. profundum:
Selection of Integration Mutants:
Validation of truB Mutants:
PCR Verification:
Functional Validation:
Phenotypic Analysis:
Test growth under varying pressure conditions (0.1-70 MPa)
Compare growth rates and cell morphology of mutant versus wild-type strains
Assess competitive fitness in co-culture experiments
Complementation Tests:
This comprehensive approach will allow researchers to establish the specific role of truB in P. profundum's adaptation to high-pressure environments.
Studying enzyme kinetics under pressure requires specialized equipment and experimental approaches. The following methodologies are recommended for investigating truB activity under varying pressure conditions:
High-Pressure Enzyme Kinetics Methods:
Stopped-Flow Spectroscopy Under Pressure:
Utilize high-pressure stopped-flow apparatus with sapphire windows
Monitor reaction progress using fluorescence detection if possible
Determine initial reaction rates at different substrate concentrations
Calculate kinetic parameters (Km, kcat) at various pressures
Plot activation volume (ΔV‡) based on pressure effects on rate constants
Real-Time NMR Under Pressure:
Use specialized high-pressure NMR cells
Monitor reaction progress directly through chemical shift changes
Determine rate constants at various pressures
Particularly useful for studying the isomerization reaction catalyzed by truB
High-Pressure Quench-Flow System:
React enzyme and substrate under pressure
Rapidly quench at defined time points
Analyze reaction products after depressurization
Use HPLC or mass spectrometry for product quantification
Determine reaction rates at different pressures
Comparative Analysis Approach:
Perform parallel experiments with truB from P. profundum and non-piezophilic organisms
Compare pressure dependence of kinetic parameters
Identify differences that may relate to pressure adaptation
Data Analysis and Interpretation:
The pressure dependence of reaction rate constants (k) can be analyzed using the transition state theory equation:
Where:
ΔV‡ is the activation volume
R is the gas constant
T is absolute temperature
P is pressure
Negative activation volumes indicate that pressure accelerates the reaction, while positive values indicate inhibition by pressure. For truB from piezophilic organisms like P. profundum, you might expect smaller positive (or even negative) activation volumes compared to enzymes from non-piezophilic sources, reflecting adaptation to high-pressure environments.
Research on P. profundum truB offers unique insights that extend beyond this specific enzyme to broader understanding of RNA modification systems:
Evolutionary Adaptations in RNA Modification Enzymes:
P. profundum truB represents an adaptation of a conserved RNA modification system to extreme conditions
Comparative analysis with homologs from organisms living at different pressures can reveal how RNA modification enzymes evolve under selective pressure
This provides a natural experiment for understanding the evolutionary plasticity of RNA modification systems
Functional Importance of RNA Modifications Under Stress:
While truB deletion in E. coli only affects growth under stress conditions, its potential essentiality for high-pressure growth in piezophiles would highlight the critical nature of RNA modifications under extreme conditions
This may reveal previously unappreciated roles of specific RNA modifications in cellular stress responses
Structural Stability Mechanisms in RNA:
Understanding how pseudouridine modifications contribute to tRNA stability under pressure offers insights into fundamental principles of RNA stabilization
These principles may apply to other structured RNAs and have implications for RNA-based therapeutics and technologies
Translation Systems Engineering:
Insights from piezophilic truB could inform the design of translation systems functioning under non-standard conditions
Applications may include cold-adapted or pressure-resistant protein expression systems for biotechnology
To comprehensively assess how truB-mediated tRNA modifications affect translation under pressure, researchers should employ multi-omics approaches:
1. Ribosome Profiling Under Pressure:
Culture cells (wild-type and truB mutants) under various pressure conditions
Treat with antibiotics that freeze ribosomes on mRNA
Isolate ribosome-protected fragments
Sequence to determine ribosome positions genome-wide
Analyze translation efficiency and pausing at specific codons
Compare translation profiles between wild-type and truB mutant strains
2. Proteomics Analysis:
Perform quantitative proteomics on wild-type and truB mutant strains grown under different pressure conditions
Identify differentially expressed proteins
Look for patterns related to specific codon usage or mRNA structural features
Correlate with transcriptomics data to distinguish translational from transcriptional effects
3. tRNA Modification Analysis:
Isolate total tRNA from cells grown under different pressure conditions
Analyze the complete set of tRNA modifications using mass spectrometry
Compare modification profiles between atmospheric and high-pressure conditions
Quantify changes in pseudouridylation at position 55 and potential compensatory modifications
4. In vitro Translation Systems:
Develop cell-free translation systems using components from P. profundum
Compare translation efficiency using native tRNAs versus tRNAs lacking pseudouridine modifications
Perform experiments under varying pressure conditions in specialized high-pressure vessels
Measure translation rates and accuracy under different conditions
5. Codon-Specific Translation Efficiency:
Design reporter constructs with different codon usage patterns
Express in wild-type and truB mutant strains under various pressure conditions
Quantify protein output and correlate with codon usage
Identify whether specific codons are more affected by the absence of truB activity
These approaches would provide a comprehensive understanding of how truB-mediated tRNA modifications contribute to translation efficiency under pressure, potentially revealing codon-specific effects and mechanisms of translational adaptation to high-pressure environments.
Structural studies of P. profundum truB could provide valuable insights for the rational design of pressure-adapted enzymes for biotechnological applications:
Key Structural Features with Engineering Implications:
Cavity Architecture:
High-pressure adapted proteins often have reduced internal cavities
Mapping the void volumes in P. profundum truB and comparing with non-piezophilic homologs
This information could guide protein engineering approaches for filling cavities in pressure-sensitive enzymes
Flexibility and Rigidity Distribution:
Pressure-adapted enzymes often have altered distribution of rigid and flexible regions
Structural analysis of B-factors and molecular dynamics simulations
Identifying flexible regions that allow conformational adaptation without compromising catalytic function
Surface Hydration Properties:
Pressure affects protein-water interactions and hydration layers
Analyzing surface charge distribution and hydrophobic/hydrophilic patches
Engineering surface properties to optimize function under pressure
Salt Bridges and Electrostatic Interactions:
Pressure-adapted proteins often have increased numbers of ion pairs
Identifying unique salt bridge networks in P. profundum truB
Implementing similar stabilizing interactions in other enzymes
Engineering Applications:
Biocatalysis Under Pressure:
High-pressure processes can offer advantages in industrial biocatalysis
Engineered pressure-resistant enzymes could expand the operating conditions for biocatalytic processes
Principles from P. profundum truB could guide development of pressure-stable biocatalysts
Cold-Adapted Enzymes:
Many principles of pressure adaptation overlap with cold adaptation
Structural insights could inform the development of enzymes for low-temperature applications
Combined pressure and cold adaptation for specific industrial processes
Protein Therapeutics Stability:
Principles of structural stability under pressure could improve storage stability of protein therapeutics
Engineering longer shelf-life and stress resistance into protein drugs
Structure-Based Design Strategy:
Develop a systematic approach for pressure-adapting enzymes based on truB structural features
Create a pressure-adaptation "toolkit" of structural modifications
Apply to industrially relevant enzymes to improve their performance under non-standard conditions
Recent cryo-EM studies of other proteins from P. profundum, such as the SiaQM transporter , have demonstrated the value of structural approaches for understanding piezophilic adaptations. Similar high-resolution structural studies of truB would significantly advance the field of enzyme engineering for extreme conditions.
While the available search results don't provide comprehensive information about all tRNA modification enzymes in P. profundum specifically, we can make evidence-based comparisons based on known patterns in related organisms:
Comparative Analysis of tRNA Modification Systems:
| Enzyme | Modification | Position | Bacterial Function | Piezophilic Adaptation |
|---|---|---|---|---|
| TruB | Pseudouridine (Ψ) | Position 55 | tRNA stability, stress response | Likely maintained function under pressure |
| TruA | Pseudouridine (Ψ) | Positions 38-40 | Anticodon loop flexibility | Unknown adaptation status |
| TrmA | 5-methyluridine (m⁵U) | Position 54 | Adjacent to TruB target | Synergistic function with TruB |
| TrmD | 1-methylguanosine (m¹G) | Position 37 | Reading frame maintenance | Unknown adaptation status |
| TrmL | 2'-O-methylcytidine (Cm) | Various positions | Structural stabilization | Potential pressure-specific modifications |
In P. profundum, truB likely plays a particularly important role compared to other tRNA modification enzymes because:
The pseudouridine at position 55 is one of the most universally conserved RNA modifications, suggesting fundamental importance
Studies in E. coli have shown that combining truB mutations with mutations affecting TrmA (which modifies the adjacent position 54) significantly increases temperature sensitivity , suggesting functional interaction between these modifications
In A. dieselolei, truB was among the most upregulated genes under pressure conditions , indicating potential specialization for high-pressure adaptation
Other piezophilic bacteria may have evolved different strategies for stabilizing tRNA, potentially involving different modification patterns or enzyme activities
The specific constellation of tRNA modifications in P. profundum likely represents an adapted system that maintains translation efficiency under high-pressure conditions. Detailed comparative analysis of the complete set of tRNA modifications in P. profundum grown under different pressure conditions would provide further insights into this specialized system.
Potential Interaction Mechanisms:
Modification Hierarchy:
In many RNA modification pathways, the presence of one modification can affect the efficiency of subsequent modifications
The pseudouridine at position 55 introduced by truB might create structural conditions necessary for other modifications
Under pressure conditions, this hierarchy might be particularly important for maintaining tRNA function
Compensatory Modifications:
In the absence of truB activity, other modification enzymes might increase activity to compensate
For example, adjacent modifications like m⁵U54 (introduced by TrmA) might be upregulated
These compensatory mechanisms could be pressure-dependent
Co-regulation of Modification Enzymes:
Research Approaches to Study Interactions:
Multi-enzyme Deletion Studies:
Generate single and combined deletions of truB and other RNA modification enzymes
Test growth and translation efficiency under various pressure conditions
Look for synthetic phenotypes that reveal functional interactions
RNA Modification Profiling:
Use mass spectrometry to profile all tRNA modifications in wild-type and truB mutant strains
Compare modification patterns under atmospheric versus high-pressure conditions
Identify modifications that change in response to truB deletion
Protein-Protein Interaction Studies:
Use co-immunoprecipitation or bacterial two-hybrid systems to identify proteins that interact with truB
Determine whether these interactions are pressure-dependent
Look for potential modification enzyme complexes
Transcriptional Network Analysis:
Examine co-expression patterns of RNA modification enzymes under pressure
Identify potential shared regulatory mechanisms
Map the RNA modification stress response network
The study of interaction networks among RNA modification enzymes under pressure represents an important frontier in understanding piezophilic adaptation mechanisms, with truB likely playing a central role in this network.
Based on current knowledge gaps and potential applications, several high-priority research directions emerge for P. profundum truB:
Structure-Function Relationships Under Pressure:
Determine high-resolution structures of P. profundum truB under varying pressure conditions
Identify pressure-sensing regions within the enzyme
Elucidate the molecular mechanisms of maintained catalytic activity under pressure
Systematic Mutagenesis Studies:
Create point mutations in P. profundum truB to identify residues critical for pressure adaptation
Engineer pressure-sensitivity into the enzyme to create pressure-sensing variants
Test chimeric enzymes with domains from piezophilic and non-piezophilic homologs
Transcriptome-Wide Impact of truB:
Analyze ribosome profiling data from wild-type and truB mutant strains under pressure
Identify specific mRNAs whose translation is most affected by loss of truB activity
Determine whether pressure adaptation involves specialized translation of specific stress-response genes
Evolutionary Studies:
Compare truB sequences across marine bacteria from different depths
Identify convergent adaptations to high pressure in different bacterial lineages
Reconstruct the evolutionary history of pressure adaptation in tRNA modification systems
Systems Biology Approach:
Map the complete network of RNA modifications and their interactions under pressure
Model how these modification networks respond to changing environmental conditions
Develop predictive frameworks for understanding adaptation to extreme environments
These research directions would not only advance our understanding of P. profundum truB specifically but would also contribute to broader knowledge about RNA biology, extremophile adaptations, and the fundamental principles of protein function under non-standard conditions.
The study of P. profundum truB offers several promising avenues for biotechnological applications related to deep-sea environments:
Pressure-Resistant Enzyme Technologies:
Principles derived from truB structure could inform the design of pressure-stable enzymes
Applications in deep-sea resource utilization and bioremediation
Development of biocatalysts for high-pressure industrial processes
Expression Systems for Deep-Sea Environments:
Creation of pressure-adapted protein expression systems incorporating truB and related components
In situ protein production for deep-sea applications
Biotechnological tools for studying deep-sea ecosystems
RNA-Based Technologies:
Development of pressure-stable RNA-based therapeutics or diagnostic tools
RNA storage and delivery systems incorporating stability principles from tRNA modifications
RNA catalysts (ribozymes) with enhanced stability under extreme conditions
Biomimetic Materials:
Design of pressure-resistant biomaterials inspired by molecular adaptations in piezophiles
Self-assembling systems that respond to pressure changes
Nanomaterials with pressure-dependent properties for sensing applications
Bioremediation Applications:
Engineered microorganisms with enhanced performance under deep-sea conditions
Oil-spill remediation technologies incorporating pressure-adapted enzymes
Degradation of pollutants at high pressure and low temperature